PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2O6H
Asym. Unit
Info
Asym.Unit (121 KB)
Biol.Unit 1 (115 KB)
Biol.Unit 2 (227 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LUMAZINE SYNTHASE RIBH1 FROM BRUCELLA MELITENSIS (GENE BMEI1187, SWISS-PROT ENTRY Q8YGH2) COMPLEXED WITH INHIBITOR 5-NITRO-6-(D-RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE
Authors
:
S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Br A. Bacher, M. Fischer, F. A. Goldbaum
Date
:
07 Dec 06 (Deposition) - 14 Aug 07 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: A,B,C,D,E (2x)
Keywords
:
Lumazine Synthase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Braden, A. Bacher, M. Fischer, F. A. Goldbaum
Structural And Kinetic Properties Of Lumazine Synthase Isoenzymes In The Order Rhizobiales
J. Mol. Biol. V. 373 664 2007
[
close entry info
]
Hetero Components
(2, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIa)
2b: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIb)
2c: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIc)
2d: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INId)
2e: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
INI
5
Mod. Residue
5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:67 , GLU A:73 , ALA E:67 , GLU E:73
BINDING SITE FOR RESIDUE CA A 301
02
AC2
SOFTWARE
GLU A:124
BINDING SITE FOR RESIDUE CA A 302
03
AC3
SOFTWARE
ALA B:67 , GLU B:73 , ALA D:67 , GLU D:73
BINDING SITE FOR RESIDUE CA B 303
04
AC4
SOFTWARE
ALA C:67 , GLU C:73
BINDING SITE FOR RESIDUE CA C 304
05
AC5
SOFTWARE
HOH A:404 , GLU C:124
BINDING SITE FOR RESIDUE CA C 305
06
AC6
SOFTWARE
ASP D:24 , ASP D:25 , ASP D:28 , HOH D:484
BINDING SITE FOR RESIDUE CA D 306
07
AC7
SOFTWARE
PHE A:22 , TYR A:23 , GLY A:52 , ALA A:53 , LEU A:54 , GLU A:55 , THR A:82 , VAL A:83 , HIS A:90 , VAL A:94 , HOH A:403 , ASN E:115 , PHE E:140
BINDING SITE FOR RESIDUE INI A 201
08
AC8
SOFTWARE
ASN A:115 , PHE A:140 , PHE B:22 , TYR B:23 , GLY B:52 , ALA B:53 , LEU B:54 , GLU B:55 , THR B:82 , VAL B:83 , ILE B:84 , HIS B:90 , VAL B:94 , HOH B:422
BINDING SITE FOR RESIDUE INI B 202
09
AC9
SOFTWARE
GLY B:114 , ASN B:115 , PHE B:140 , ALA B:144 , PHE C:22 , TYR C:23 , GLY C:52 , ALA C:53 , LEU C:54 , GLU C:55 , THR C:82 , VAL C:83 , ILE C:84 , HIS C:90 , VAL C:94 , HOH C:438
BINDING SITE FOR RESIDUE INI C 203
10
BC1
SOFTWARE
ASN C:115 , PHE C:140 , PHE D:22 , TYR D:23 , GLY D:52 , ALA D:53 , LEU D:54 , GLU D:55 , THR D:82 , VAL D:83 , ILE D:84 , HIS D:90 , VAL D:94
BINDING SITE FOR RESIDUE INI D 204
11
BC2
SOFTWARE
ASN D:115 , PHE D:140 , PHE E:22 , TYR E:23 , GLY E:52 , ALA E:53 , LEU E:54 , GLU E:55 , THR E:82 , VAL E:83 , ILE E:84 , HIS E:90 , VAL E:94
BINDING SITE FOR RESIDUE INI E 205
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_2o6hA00 (A:11-157)
1b: CATH_2o6hB00 (B:11-157)
1c: CATH_2o6hD00 (D:11-157)
1d: CATH_2o6hE00 (E:11-157)
1e: CATH_2o6hC00 (C:12-157)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.960, no name defined]
(36)
Brucella melitensis. Organism_taxid: 29459.
(1)
1a
2o6hA00
A:11-157
1b
2o6hB00
B:11-157
1c
2o6hD00
D:11-157
1d
2o6hE00
E:11-157
1e
2o6hC00
C:12-157
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_DMRL_synthase_2o6hE01 (E:11-155)
1b: PFAM_DMRL_synthase_2o6hE02 (E:11-155)
1c: PFAM_DMRL_synthase_2o6hE03 (E:11-155)
1d: PFAM_DMRL_synthase_2o6hE04 (E:11-155)
1e: PFAM_DMRL_synthase_2o6hE05 (E:11-155)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DMRL_synthase]
(19)
Family
:
DMRL_synthase
(19)
Brucella melitensis
(1)
1a
DMRL_synthase-2o6hE01
E:11-155
1b
DMRL_synthase-2o6hE02
E:11-155
1c
DMRL_synthase-2o6hE03
E:11-155
1d
DMRL_synthase-2o6hE04
E:11-155
1e
DMRL_synthase-2o6hE05
E:11-155
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (121 KB)
Header - Asym.Unit
Biol.Unit 1 (115 KB)
Header - Biol.Unit 1
Biol.Unit 2 (227 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2O6H
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help